User:Lindsay V. Clark: Difference between revisions

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[[Image:LindsayClarkface.jpg|thumb|left|Lindsay V. Clark]]
[[Image:LindsayClarkface2.jpg|thumb|left|Lindsay V. Clark]]


I am a plant population and ecological geneticist in the final stages of my Ph.D.  I am available to start work as a post-doc on July 1, 2011.  If you like what you see here, feel free to contact me with any openings or potential openings that you may have in your lab!
'''Postdoctoral Research Associate, Plant Population Genetics'''
 
'''Energy Biosciences Institute'''
 
'''University of Illinois, Urbana-Champaign'''


== Research and Personal Info ==
== Research and Personal Info ==


I'm a fifth-year Ph.D. student in the [[UC Davis Genetics Graduate Group|Genetics Graduate Group at UC Davis]], and a member of the [[Jasieniuk]] lab in the Department of Plant Sciences.  My research interest is in the evolution of invasiveness in plants through hybridization and changes in gene expression.  My study organism is Himalayan blackberry, an introduced species from Europe that is highly invasive on the West Coast and is known to hybridize with native and other introduced species.
I am a postdoc studying the genetic diversity and population structure of ''Miscanthus'', a perennial grass being developed as a bioenergy crop, under [http://cropsci.illinois.edu/directory/esacks Dr. Erik Sacks] at the University of Illinois, Urbana-Champaign.
 
I recently finished my Ph.D. (September 2011) in the [[UC Davis Genetics Graduate Group|Genetics Graduate Group at UC Davis]] as a member of the [[Jasieniuk]] lab in the Department of Plant Sciences.  My dissertation research was on the evolution of invasiveness in blackberry (''Rubus''), particularly relating to hybridization and asexual reproduction.  I have also written software in R for the analysis of polyploid data.


I graduated from Dartmouth College in 2004, having majored in Genetics, Cell & Developmental Biology and minored in Chemistry.  From June 2002 to June 2004 I did my undergraduate thesis research in [http://www.dartmouth.edu/~tjack/ Thomas Jack's lab], where I worked on developing knockout mutants for a gene family putatively involved in floral development in ''Arabidopsis''.
I graduated from Dartmouth College in 2004, having majored in Genetics, Cell & Developmental Biology and minored in Chemistry.  From June 2002 to June 2004 I did my undergraduate thesis research in [http://www.dartmouth.edu/~tjack/ Thomas Jack's lab], where I worked on developing knockout mutants for a gene family putatively involved in floral development in ''Arabidopsis''.
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From November 2004 - July 2006 I worked at the [http://www.ars.usda.gov/Main/site_main.htm?modecode=19-10-10-00 Grape Genetics Research Unit] in Geneva, NY.  Under the direction of Amanda Garris, I worked on gene cloning and QTL mapping towards an understanding of light detection and winter dormancy in grapevine.
From November 2004 - July 2006 I worked at the [http://www.ars.usda.gov/Main/site_main.htm?modecode=19-10-10-00 Grape Genetics Research Unit] in Geneva, NY.  Under the direction of Amanda Garris, I worked on gene cloning and QTL mapping towards an understanding of light detection and winter dormancy in grapevine.


[[Image:Prickleyfoe.JPG|400 px|right|Surrounded by my prickly nemesis.]]
[[Image:plantintube.JPG|200 px|right]]


Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
Contact: [[Special:Emailuser/Lindsay_V._Clark|email]]
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[http://www.researcherid.com/rid/B-3165-2008 ResearcherID]
[http://www.researcherid.com/rid/B-3165-2008 ResearcherID]


[http://ucdavis.academia.edu/LindsayClark Academia.edu profile with CV]
[http://ucdavis.academia.edu/LindsayClark Academia.edu profile]
 
[[Media:lvclark_CV_2011_December13.pdf|Curriculum Vitae]]


== Publications ==
== Publications ==
* Lindsay V. Clark and Marie Jasieniuk (2011) "POLYSAT: an R package for polyploid microsatellite analysis."  Molecular Ecology Resources (in press).
* Lindsay V. Clark and Marie Jasieniuk (2011) "POLYSAT: an R package for polyploid microsatellite analysis."  Molecular Ecology Resources 11(3):562-566.  [[doi:10.1111/j.1755-0998.2011.02985.x]]
* Lindsay V. Clark and Marie Jasieniuk (2012) "Spontaneous hybrids between native and exotic ''Rubus'' in the Western United States produce offspring both by apomixis and by sexual recombination."  Heredity 109(5):320-328.  [[doi:10.1038/hdy.2012.45]]
* Lindsay V. Clark, Katherine J. Evans, and Marie Jasieniuk "Origins and distribution of invasive ''Rubus fruticosus'' L. agg. (Rosaceae) clones in the Western United States."  Biological Invasions (in press). [[doi:10.1007/s10530-012-0369-8]]
*Amanda Garris, Lindsay Clark, Chris Owens, Steven McKay, James Luby, Kathy Mathiason, and Anne Fennell (2009) [http://journal.ashspublications.org/cgi/content/abstract/134/2/261 "Mapping of Photoperiod-Induced Growth Cessation in the Wild Grape ''Vitis riparia'' Michx."] Journal of the American Society for Horticultural Science 134:261-272.
*Amanda Garris, Lindsay Clark, Chris Owens, Steven McKay, James Luby, Kathy Mathiason, and Anne Fennell (2009) [http://journal.ashspublications.org/cgi/content/abstract/134/2/261 "Mapping of Photoperiod-Induced Growth Cessation in the Wild Grape ''Vitis riparia'' Michx."] Journal of the American Society for Horticultural Science 134:261-272.


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[[polysat]]: tools for polyploid microsatellite analysis
[[polysat]]: tools for polyploid microsatellite analysis


==Awards==
===Handy scripts===
*Plant Sciences Departmental Research Assistantship
*Convert TASSEL's HapMap format to adegenet's genlight format: [[Media:hapMap2genlight.R.txt]]
*Jastro-Shields Research Grant
*Convert TASSEL's HapMap format to adegenet's genind format: [[Media:hapMap2genind.R.txt]]
*Department of Plant Sciences Graduate Student Travel Award
*Convert adegenet's genind format to STRUCTURE format: [[Media:genind2structure.R.txt]]
*California Weed Science Society Scholarship


==Presentations==
==Presentations==
*“Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008
*"Using molecular markers to investigate invasive ''Rubus'' and genetic diversity of ''Miscanthus''".  Invited seminar speaker, Western Kentucky University Biology Department, September 7, 2012.
*[http://conferences.igb.illinois.edu/panamerican/sites/conferences.igb.illinois.edu.panamerican/files/u4/Clark_%20Bioenergy%20Congress%20presentation%202012.pdf "Genetic diversity and population structure of ''Miscanthus'' in Japan"] at the 3rd Pan American Congress on Plants and Bioenergy, Champaign, Illinois,  June 17, 2012.
*"Polyploid data analysis, and how to gently transition from software user to software developer" for UC Davis Ecological Genetics grad course, February 28, 2011 [[Media:LVC_PHR242_110228.pdf | PDF]]
*“Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008.


==Posters==
==Posters==
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*[http://www.intl-pag.org/18/abstracts/P03a_PAGXVIII_125.html "Hybridization Between Native And Introduced ''Rubus'' In California And The Pacific Northwest"] at Plant and Animal Genome XVIII, January 9-13, 2010. [[Media:LVCpag2010.pdf | PDF]]
*[http://www.intl-pag.org/18/abstracts/P03a_PAGXVIII_125.html "Hybridization Between Native And Introduced ''Rubus'' In California And The Pacific Northwest"] at Plant and Animal Genome XVIII, January 9-13, 2010. [[Media:LVCpag2010.pdf | PDF]]
*[http://www.cal-ipc.org/symposia/archive/pdf/2008/posterClark.pdf “Hybridization between invasive and native blackberries (''Rubus'') in California”] at California Invasive Plant Council Symposium, October 2-4, 2008.
*[http://www.cal-ipc.org/symposia/archive/pdf/2008/posterClark.pdf “Hybridization between invasive and native blackberries (''Rubus'') in California”] at California Invasive Plant Council Symposium, October 2-4, 2008.
==Awards==
*Plant Sciences Departmental Research Assistantship
*Jastro-Shields Research Grant
*Department of Plant Sciences Graduate Student Travel Award
*California Weed Science Society Scholarship


==Teaching experience==
==Teaching experience==
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==Protocols==
==Protocols==
*[[Sacks:RAD-seq]]
*[[Jasieniuk:Converting_codominant_to_dominant_data]]
*[[Jasieniuk:Converting_codominant_to_dominant_data]]
*[[Jasieniuk:Implementation_of_a_method_to_calculate_microsatellite_genotype_distance_in_polyploids]]
*[[Jasieniuk:Implementation_of_a_method_to_calculate_microsatellite_genotype_distance_in_polyploids]]

Revision as of 14:36, 18 March 2013

Lindsay V. Clark

Postdoctoral Research Associate, Plant Population Genetics

Energy Biosciences Institute

University of Illinois, Urbana-Champaign

Research and Personal Info

I am a postdoc studying the genetic diversity and population structure of Miscanthus, a perennial grass being developed as a bioenergy crop, under Dr. Erik Sacks at the University of Illinois, Urbana-Champaign.

I recently finished my Ph.D. (September 2011) in the Genetics Graduate Group at UC Davis as a member of the Jasieniuk lab in the Department of Plant Sciences. My dissertation research was on the evolution of invasiveness in blackberry (Rubus), particularly relating to hybridization and asexual reproduction. I have also written software in R for the analysis of polyploid data.

I graduated from Dartmouth College in 2004, having majored in Genetics, Cell & Developmental Biology and minored in Chemistry. From June 2002 to June 2004 I did my undergraduate thesis research in Thomas Jack's lab, where I worked on developing knockout mutants for a gene family putatively involved in floral development in Arabidopsis.

From November 2004 - July 2006 I worked at the Grape Genetics Research Unit in Geneva, NY. Under the direction of Amanda Garris, I worked on gene cloning and QTL mapping towards an understanding of light detection and winter dormancy in grapevine.

Contact: email

ResearcherID

Academia.edu profile

Curriculum Vitae

Publications

  • Lindsay V. Clark and Marie Jasieniuk (2011) "POLYSAT: an R package for polyploid microsatellite analysis." Molecular Ecology Resources 11(3):562-566. doi:10.1111/j.1755-0998.2011.02985.x
  • Lindsay V. Clark and Marie Jasieniuk (2012) "Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination." Heredity 109(5):320-328. doi:10.1038/hdy.2012.45
  • Lindsay V. Clark, Katherine J. Evans, and Marie Jasieniuk "Origins and distribution of invasive Rubus fruticosus L. agg. (Rosaceae) clones in the Western United States." Biological Invasions (in press). doi:10.1007/s10530-012-0369-8
  • Amanda Garris, Lindsay Clark, Chris Owens, Steven McKay, James Luby, Kathy Mathiason, and Anne Fennell (2009) "Mapping of Photoperiod-Induced Growth Cessation in the Wild Grape Vitis riparia Michx." Journal of the American Society for Horticultural Science 134:261-272.

Software

polysat: tools for polyploid microsatellite analysis

Handy scripts

Presentations

  • "Using molecular markers to investigate invasive Rubus and genetic diversity of Miscanthus". Invited seminar speaker, Western Kentucky University Biology Department, September 7, 2012.
  • "Genetic diversity and population structure of Miscanthus in Japan" at the 3rd Pan American Congress on Plants and Bioenergy, Champaign, Illinois, June 17, 2012.
  • "Polyploid data analysis, and how to gently transition from software user to software developer" for UC Davis Ecological Genetics grad course, February 28, 2011 PDF
  • “Hybridization of native and invasive blackberries in California” at UC Davis Weed Day, July 17, 2008.

Posters

Awards

  • Plant Sciences Departmental Research Assistantship
  • Jastro-Shields Research Grant
  • Department of Plant Sciences Graduate Student Travel Award
  • California Weed Science Society Scholarship

Teaching experience

  • Associate Instructor, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Summer 2009
  • Guest lecturer, Ecological Genetics, UC Davis Ecology Graduate Group, Winter 2011
  • Teaching assistant, Principles of Genetics Laboratory, UC Davis Department of Molecular and Cellular Biology, Winter 2010
  • Teaching assistant, Genes and Gene Expression, UC Davis Department of Molecular and Cellular Biology, Fall 2009, Winter 2011
  • Teaching assistant, Human Heredity, UC Davis Department of Molecular and Cellular Biology, Spring 2007, Spring 2009
  • Teaching assistant, Plant Genetics and Biotechnology Laboratory, UC Davis Department of Plant Sciences, Winter 2009
  • Undergraduate teaching assistant, Molecular Biology Lab, Dartmouth College Department of Biological Sciences, Summer 2003

Protocols

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